Molecular dynamics simulation trajectories of binding of N-acetylglucosamine
mono- ((GlcNAc)1), di- ((GlcNAc)2) and trisaccharide ((GlcNAc)3) onto hevein
domain HEV32. Systems containing one molecule of HEV32, one molecule of
an oligosaccharide and 2271-2287 water molecules were simulated for
1 microsecond. Two replicates were done for each system. Binding of
oligosaccharides into their experimentally verified binding sites was observed
in three of six simulations. Gromacs trajectories do not contain water
molecules and are are sampled every 100 ps. Gromacs structures (*.gro) and
trajectories (*.xtc) can be opened in Gromacs (analysis), Visual Molecular
Dynamics (visualization) or other software or libraries (e.g. Plumed, MDtraj).
Collective motions of the protein were analyzed by essential dynamics approach
(directory ed). These files (*gro, *trr, *pdb) can be used for analyses in
Gromacs. The eigenvalue (*.xvg) file can be visualized by Grace, Gnuplot or
any x/y plotting program or library.

mono1/after_mdp3nowater.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)1.

mono1/md_fit2.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)1.

mono2/after_mdp3nowater.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)1.

mono2/md_fit2.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)1.

di1/after_mdp3nowater.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)2.

di1/md_fit2.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)2.

di2/after_mdp3nowater.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)2.

di2/md_fit2.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)2.

tri1/after_mdp3nowater.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)3.

tri1/md_fit2.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)3.

tri2/after_mdp3nowater.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)3.

tri2/md_fit2.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)3.

ed/protein.gro
Initial protein structure for essential dynamics of protein motions.

ed/protein.xtc
Protein supertrajectory from all six simulation concatenated for essential
dynamics of protein motions.

ed/average.pdb
Average protein structure from the supertrajectory from all six simulation
concatenated for essential dynamics of protein motions.

ed/covar.log
Log file from essential dynamics of protein motions.

ed/eigenval.xvg
Eigenvalues from essential dynamics of protein motions.

ed/eigenvec.trr
Eigenvecors from essential dynamics of protein motions.

md5sum.log
MD5 sums of files.